Starting phenix.real_space_refine on Wed Jun 4 16:58:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tmc_25995/06_2025/7tmc_25995.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tmc_25995/06_2025/7tmc_25995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tmc_25995/06_2025/7tmc_25995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tmc_25995/06_2025/7tmc_25995.map" model { file = "/net/cci-nas-00/data/ceres_data/7tmc_25995/06_2025/7tmc_25995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tmc_25995/06_2025/7tmc_25995.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2178 2.51 5 N 531 2.21 5 O 696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3426 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "C" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.28, per 1000 atoms: 0.96 Number of scatterers: 3426 At special positions: 0 Unit cell: (101.184, 110.67, 35.836, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 696 8.00 N 531 7.00 C 2178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 301 " - " ASN A 151 " " NAG A 302 " - " ASN A 145 " " NAG A 303 " - " ASN A 164 " " NAG A 304 " - " ASN A 183 " " NAG B 301 " - " ASN B 151 " " NAG B 302 " - " ASN B 145 " " NAG B 303 " - " ASN B 164 " " NAG B 304 " - " ASN B 183 " " NAG C 301 " - " ASN C 151 " " NAG C 302 " - " ASN C 145 " " NAG C 303 " - " ASN C 164 " " NAG C 304 " - " ASN C 183 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 393.2 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 44.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 124 through 126 removed outlier: 6.091A pdb=" N TYR A 125 " --> pdb=" O ILE C 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 130 removed outlier: 8.001A pdb=" N SER B 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 133 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 129 through 130 removed outlier: 9.113A pdb=" N SER A 130 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N VAL C 133 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR A 132 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 141 through 143 removed outlier: 5.870A pdb=" N ILE A 142 " --> pdb=" O TYR C 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.524A pdb=" N ILE A 152 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 157 removed outlier: 6.522A pdb=" N ASN A 156 " --> pdb=" O TYR B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 169 through 175 removed outlier: 6.217A pdb=" N GLN A 170 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LYS B 173 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER A 172 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL B 175 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR A 174 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 169 " --> pdb=" O GLN C 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 175 removed outlier: 6.217A pdb=" N GLN A 170 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LYS B 173 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER A 172 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL B 175 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR A 174 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 184 through 186 removed outlier: 6.398A pdb=" N ILE A 184 " --> pdb=" O THR B 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 190 through 193 removed outlier: 6.878A pdb=" N LEU A 190 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N LYS B 193 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N MET A 192 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 196 through 197 removed outlier: 6.082A pdb=" N ASP A 196 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 206 removed outlier: 6.317A pdb=" N VAL A 202 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU C 205 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA A 204 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 209 through 218 removed outlier: 6.767A pdb=" N MET A 210 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N PHE B 213 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP A 212 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR B 215 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N CYS A 214 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N ILE B 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N LEU A 216 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR A 209 " --> pdb=" O MET C 210 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ASP C 212 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR A 211 " --> pdb=" O ASP C 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 209 through 218 removed outlier: 6.767A pdb=" N MET A 210 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N PHE B 213 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP A 212 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR B 215 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N CYS A 214 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N ILE B 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N LEU A 216 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 224 through 228 removed outlier: 6.060A pdb=" N VAL A 225 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET B 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N MET A 227 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 233 through 240 removed outlier: 6.641A pdb=" N THR A 233 " --> pdb=" O THR B 234 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N TYR B 236 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR A 235 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY B 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A 237 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N SER B 240 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N HIS A 239 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 243 through 246 removed outlier: 6.111A pdb=" N SER A 244 " --> pdb=" O GLN C 245 " (cutoff:3.500A) 37 hydrogen bonds defined for protein. 111 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.81 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1050 1.34 - 1.46: 802 1.46 - 1.58: 1592 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 3480 Sorted by residual: bond pdb=" C1 NAG C 303 " pdb=" O5 NAG C 303 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C1 NAG A 303 " pdb=" O5 NAG A 303 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1 NAG B 303 " pdb=" O5 NAG B 303 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C1 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.39e+00 bond pdb=" C1 NAG C 302 " pdb=" O5 NAG C 302 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.34e+00 ... (remaining 3475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 4252 1.10 - 2.20: 390 2.20 - 3.29: 68 3.29 - 4.39: 10 4.39 - 5.49: 11 Bond angle restraints: 4731 Sorted by residual: angle pdb=" N GLY C 238 " pdb=" CA GLY C 238 " pdb=" C GLY C 238 " ideal model delta sigma weight residual 110.29 114.60 -4.31 1.28e+00 6.10e-01 1.14e+01 angle pdb=" N ILE C 219 " pdb=" CA ILE C 219 " pdb=" C ILE C 219 " ideal model delta sigma weight residual 109.34 103.85 5.49 2.08e+00 2.31e-01 6.96e+00 angle pdb=" N ILE A 219 " pdb=" CA ILE A 219 " pdb=" C ILE A 219 " ideal model delta sigma weight residual 109.34 103.92 5.42 2.08e+00 2.31e-01 6.78e+00 angle pdb=" N GLN C 138 " pdb=" CA GLN C 138 " pdb=" C GLN C 138 " ideal model delta sigma weight residual 109.65 113.65 -4.00 1.56e+00 4.11e-01 6.59e+00 angle pdb=" N ILE B 219 " pdb=" CA ILE B 219 " pdb=" C ILE B 219 " ideal model delta sigma weight residual 109.34 104.08 5.26 2.08e+00 2.31e-01 6.40e+00 ... (remaining 4726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 2092 24.85 - 49.69: 114 49.69 - 74.54: 27 74.54 - 99.39: 7 99.39 - 124.23: 7 Dihedral angle restraints: 2247 sinusoidal: 1029 harmonic: 1218 Sorted by residual: dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 253 " pdb=" CB CYS A 253 " ideal model delta sinusoidal sigma weight residual 93.00 167.93 -74.93 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 253 " pdb=" CB CYS C 253 " ideal model delta sinusoidal sigma weight residual 93.00 163.42 -70.42 1 1.00e+01 1.00e-02 6.38e+01 dihedral pdb=" CA TYR A 143 " pdb=" C TYR A 143 " pdb=" N LEU A 144 " pdb=" CA LEU A 144 " ideal model delta harmonic sigma weight residual 180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 2244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 491 0.080 - 0.159: 102 0.159 - 0.239: 3 0.239 - 0.319: 2 0.319 - 0.399: 5 Chirality restraints: 603 Sorted by residual: chirality pdb=" C1 NAG C 304 " pdb=" ND2 ASN C 183 " pdb=" C2 NAG C 304 " pdb=" O5 NAG C 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C1 NAG B 304 " pdb=" ND2 ASN B 183 " pdb=" C2 NAG B 304 " pdb=" O5 NAG B 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C1 NAG A 304 " pdb=" ND2 ASN A 183 " pdb=" C2 NAG A 304 " pdb=" O5 NAG A 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 600 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 199 " 0.056 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO C 200 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 145 " 0.026 2.00e-02 2.50e+03 2.41e-02 7.28e+00 pdb=" CG ASN B 145 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B 145 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 145 " -0.024 2.00e-02 2.50e+03 pdb=" C1 NAG B 302 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 199 " 0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO B 200 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " 0.034 5.00e-02 4.00e+02 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 99 2.70 - 3.25: 3219 3.25 - 3.80: 5135 3.80 - 4.35: 6307 4.35 - 4.90: 11312 Nonbonded interactions: 26072 Sorted by model distance: nonbonded pdb=" OG1 THR C 231 " pdb=" OG1 THR C 234 " model vdw 2.152 3.040 nonbonded pdb=" OD2 ASP A 196 " pdb=" OG1 THR A 198 " model vdw 2.193 3.040 nonbonded pdb=" NZ LYS B 129 " pdb=" OD2 ASP B 136 " model vdw 2.201 3.120 nonbonded pdb=" OD1 ASP B 212 " pdb=" OG1 THR B 215 " model vdw 2.214 3.040 nonbonded pdb=" NE2 GLN C 249 " pdb=" OD2 ASP C 252 " model vdw 2.225 3.120 ... (remaining 26067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.200 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3031 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 3495 Z= 0.252 Angle : 0.882 12.758 4773 Z= 0.417 Chirality : 0.066 0.399 603 Planarity : 0.006 0.085 570 Dihedral : 18.016 124.235 1458 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 239 PHE 0.005 0.001 PHE A 237 TYR 0.022 0.002 TYR B 250 ARG 0.001 0.000 ARG B 247 Details of bonding type rmsd link_NAG-ASN : bond 0.00785 ( 12) link_NAG-ASN : angle 5.84237 ( 36) hydrogen bonds : bond 0.19135 ( 36) hydrogen bonds : angle 8.56774 ( 111) SS BOND : bond 0.00509 ( 3) SS BOND : angle 1.54108 ( 6) covalent geometry : bond 0.00539 ( 3480) covalent geometry : angle 0.72249 ( 4731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 TYR cc_start: 0.2725 (m-80) cc_final: 0.2105 (p90) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1570 time to fit residues: 19.2980 Evaluate side-chains 65 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN B 249 GLN C 155 ASN C 170 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.158940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.144770 restraints weight = 5835.046| |-----------------------------------------------------------------------------| r_work (start): 0.4531 rms_B_bonded: 3.32 r_work: 0.4443 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 1.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 3495 Z= 0.333 Angle : 1.330 14.809 4773 Z= 0.608 Chirality : 0.083 0.587 603 Planarity : 0.007 0.065 570 Dihedral : 12.993 59.405 699 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.79 % Favored : 85.21 % Rotamer: Outliers : 4.76 % Allowed : 15.87 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 222 PHE 0.015 0.002 PHE C 213 TYR 0.033 0.003 TYR A 197 ARG 0.003 0.001 ARG C 140 Details of bonding type rmsd link_NAG-ASN : bond 0.01962 ( 12) link_NAG-ASN : angle 7.02906 ( 36) hydrogen bonds : bond 0.02212 ( 36) hydrogen bonds : angle 6.43253 ( 111) SS BOND : bond 0.00330 ( 3) SS BOND : angle 1.00018 ( 6) covalent geometry : bond 0.00727 ( 3480) covalent geometry : angle 1.18595 ( 4731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.8080 (mt) cc_final: 0.7583 (tt) REVERT: A 242 GLN cc_start: 0.7149 (pt0) cc_final: 0.6605 (tt0) REVERT: B 144 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6616 (tt) REVERT: B 194 GLN cc_start: 0.7236 (mt0) cc_final: 0.6931 (tp-100) REVERT: B 222 HIS cc_start: 0.6941 (m-70) cc_final: 0.6688 (m90) REVERT: B 246 GLU cc_start: 0.7076 (pt0) cc_final: 0.6474 (tp30) REVERT: C 135 TYR cc_start: 0.3077 (OUTLIER) cc_final: 0.2369 (m-10) REVERT: C 180 ARG cc_start: 0.6966 (mtt180) cc_final: 0.6418 (ptt-90) outliers start: 18 outliers final: 9 residues processed: 159 average time/residue: 0.1321 time to fit residues: 25.7372 Evaluate side-chains 134 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 208 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN C 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.138264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.124769 restraints weight = 6135.597| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 3.00 r_work: 0.4215 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 1.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 3495 Z= 0.278 Angle : 1.187 14.225 4773 Z= 0.542 Chirality : 0.072 0.444 603 Planarity : 0.006 0.081 570 Dihedral : 10.881 56.073 699 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 6.88 % Allowed : 20.37 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.022 0.003 PHE A 237 TYR 0.020 0.003 TYR C 135 ARG 0.007 0.001 ARG C 140 Details of bonding type rmsd link_NAG-ASN : bond 0.01498 ( 12) link_NAG-ASN : angle 7.19570 ( 36) hydrogen bonds : bond 0.03044 ( 36) hydrogen bonds : angle 5.72705 ( 111) SS BOND : bond 0.00812 ( 3) SS BOND : angle 1.09077 ( 6) covalent geometry : bond 0.00622 ( 3480) covalent geometry : angle 1.01247 ( 4731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8631 (mttm) cc_final: 0.8189 (mmtp) REVERT: A 138 GLN cc_start: 0.8053 (mm110) cc_final: 0.7575 (mm-40) REVERT: A 163 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8444 (mm-30) REVERT: A 164 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7230 (m-40) REVERT: A 193 LYS cc_start: 0.7341 (mmtt) cc_final: 0.7009 (mtmm) REVERT: A 194 GLN cc_start: 0.8011 (mp10) cc_final: 0.6990 (mp10) REVERT: B 163 GLU cc_start: 0.4158 (pm20) cc_final: 0.3091 (mm-30) REVERT: B 180 ARG cc_start: 0.3065 (mmp-170) cc_final: 0.2696 (mmp-170) REVERT: B 191 ASP cc_start: 0.7943 (m-30) cc_final: 0.7063 (t0) REVERT: B 194 GLN cc_start: 0.7829 (mt0) cc_final: 0.7585 (mp10) REVERT: B 219 ILE cc_start: 0.8449 (mm) cc_final: 0.8229 (mm) REVERT: B 246 GLU cc_start: 0.8041 (pt0) cc_final: 0.7103 (tp30) REVERT: B 247 ARG cc_start: 0.8515 (ttt180) cc_final: 0.5697 (pmt-80) REVERT: C 124 LYS cc_start: 0.8438 (mttm) cc_final: 0.7944 (mmtt) REVERT: C 128 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8097 (t) REVERT: C 180 ARG cc_start: 0.7204 (mtt180) cc_final: 0.6276 (ptt-90) REVERT: C 193 LYS cc_start: 0.8157 (mtmm) cc_final: 0.7096 (mtpt) REVERT: C 194 GLN cc_start: 0.8331 (mt0) cc_final: 0.7463 (mp10) REVERT: C 216 LEU cc_start: 0.8433 (pt) cc_final: 0.8133 (pp) outliers start: 26 outliers final: 17 residues processed: 155 average time/residue: 0.1601 time to fit residues: 29.5024 Evaluate side-chains 143 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 242 GLN A 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.134193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.121493 restraints weight = 6240.797| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 3.15 r_work: 0.4191 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 1.9039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3495 Z= 0.240 Angle : 1.008 13.171 4773 Z= 0.479 Chirality : 0.069 0.549 603 Planarity : 0.007 0.080 570 Dihedral : 9.487 47.163 699 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.53 % Favored : 86.47 % Rotamer: Outliers : 8.47 % Allowed : 20.11 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 239 PHE 0.014 0.002 PHE B 171 TYR 0.033 0.002 TYR A 143 ARG 0.005 0.001 ARG A 140 Details of bonding type rmsd link_NAG-ASN : bond 0.01080 ( 12) link_NAG-ASN : angle 6.04757 ( 36) hydrogen bonds : bond 0.01900 ( 36) hydrogen bonds : angle 5.54443 ( 111) SS BOND : bond 0.00453 ( 3) SS BOND : angle 0.88420 ( 6) covalent geometry : bond 0.00512 ( 3480) covalent geometry : angle 0.86391 ( 4731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8658 (t0) cc_final: 0.8414 (t0) REVERT: A 124 LYS cc_start: 0.9024 (mttm) cc_final: 0.8687 (mmtp) REVERT: A 138 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8055 (mm-40) REVERT: A 185 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.7741 (p) REVERT: A 194 GLN cc_start: 0.8317 (mp10) cc_final: 0.7786 (mp10) REVERT: A 212 ASP cc_start: 0.7170 (m-30) cc_final: 0.6844 (m-30) REVERT: A 223 ASN cc_start: 0.8893 (t0) cc_final: 0.8624 (t0) REVERT: B 136 ASP cc_start: 0.7436 (t0) cc_final: 0.7216 (t0) REVERT: B 180 ARG cc_start: 0.3698 (mmp-170) cc_final: 0.2854 (mmp-170) REVERT: B 185 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8241 (p) REVERT: B 192 MET cc_start: 0.8179 (mpp) cc_final: 0.7902 (mpt) REVERT: B 209 TYR cc_start: 0.4418 (OUTLIER) cc_final: 0.2880 (t80) REVERT: B 210 MET cc_start: 0.7586 (tpt) cc_final: 0.7379 (tpp) REVERT: B 246 GLU cc_start: 0.8649 (pt0) cc_final: 0.7074 (tp30) REVERT: C 161 GLU cc_start: 0.8369 (tp30) cc_final: 0.8129 (tp30) REVERT: C 181 LEU cc_start: 0.6404 (mt) cc_final: 0.6201 (mp) REVERT: C 194 GLN cc_start: 0.8862 (mt0) cc_final: 0.8510 (mp10) REVERT: C 212 ASP cc_start: 0.7568 (m-30) cc_final: 0.7168 (m-30) REVERT: C 227 MET cc_start: 0.8978 (mpp) cc_final: 0.8504 (mtm) outliers start: 32 outliers final: 20 residues processed: 143 average time/residue: 0.1611 time to fit residues: 27.4160 Evaluate side-chains 126 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.137455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.124496 restraints weight = 6369.778| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 3.13 r_work: 0.4190 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 1.9489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3495 Z= 0.167 Angle : 0.907 12.633 4773 Z= 0.429 Chirality : 0.064 0.426 603 Planarity : 0.006 0.069 570 Dihedral : 8.870 52.945 699 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 6.88 % Allowed : 23.54 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 239 PHE 0.031 0.003 PHE B 171 TYR 0.023 0.002 TYR A 143 ARG 0.008 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.01029 ( 12) link_NAG-ASN : angle 5.73514 ( 36) hydrogen bonds : bond 0.01774 ( 36) hydrogen bonds : angle 5.03514 ( 111) SS BOND : bond 0.00456 ( 3) SS BOND : angle 0.87525 ( 6) covalent geometry : bond 0.00373 ( 3480) covalent geometry : angle 0.76024 ( 4731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8698 (mttm) cc_final: 0.8352 (mmtp) REVERT: A 136 ASP cc_start: 0.6880 (t0) cc_final: 0.6647 (t0) REVERT: A 138 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8256 (mm-40) REVERT: A 185 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7683 (p) REVERT: A 193 LYS cc_start: 0.8454 (mppt) cc_final: 0.7885 (mppt) REVERT: A 210 MET cc_start: 0.8339 (tpt) cc_final: 0.7799 (tpp) REVERT: A 216 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8404 (pp) REVERT: A 223 ASN cc_start: 0.8963 (t0) cc_final: 0.8594 (t0) REVERT: B 136 ASP cc_start: 0.7683 (t0) cc_final: 0.6951 (t0) REVERT: B 138 GLN cc_start: 0.8333 (mt0) cc_final: 0.8074 (mm-40) REVERT: B 180 ARG cc_start: 0.3240 (mmp-170) cc_final: 0.2484 (mmp-170) REVERT: B 185 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8373 (p) REVERT: B 192 MET cc_start: 0.8136 (mpp) cc_final: 0.7918 (mpt) REVERT: B 193 LYS cc_start: 0.4334 (mmtm) cc_final: 0.4064 (mttp) REVERT: B 194 GLN cc_start: 0.8556 (mt0) cc_final: 0.7909 (mp10) REVERT: B 209 TYR cc_start: 0.4328 (OUTLIER) cc_final: 0.2820 (t80) REVERT: B 246 GLU cc_start: 0.8670 (pt0) cc_final: 0.6888 (tp30) REVERT: C 161 GLU cc_start: 0.8500 (tp30) cc_final: 0.8296 (mm-30) REVERT: C 187 ILE cc_start: 0.8031 (mm) cc_final: 0.7506 (pt) REVERT: C 194 GLN cc_start: 0.8927 (mt0) cc_final: 0.8607 (mp10) REVERT: C 199 VAL cc_start: 0.7185 (OUTLIER) cc_final: 0.6936 (p) REVERT: C 207 MET cc_start: 0.7290 (tpt) cc_final: 0.6867 (ttp) REVERT: C 212 ASP cc_start: 0.7701 (m-30) cc_final: 0.7463 (m-30) outliers start: 26 outliers final: 20 residues processed: 130 average time/residue: 0.1668 time to fit residues: 26.0544 Evaluate side-chains 134 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.4980 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.131814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.119310 restraints weight = 6160.134| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.93 r_work: 0.4142 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 2.0294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3495 Z= 0.190 Angle : 0.917 12.491 4773 Z= 0.431 Chirality : 0.066 0.440 603 Planarity : 0.006 0.071 570 Dihedral : 8.430 49.700 699 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 7.41 % Allowed : 25.66 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 239 PHE 0.026 0.002 PHE B 171 TYR 0.017 0.002 TYR A 143 ARG 0.004 0.001 ARG C 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00949 ( 12) link_NAG-ASN : angle 5.87879 ( 36) hydrogen bonds : bond 0.01667 ( 36) hydrogen bonds : angle 4.99036 ( 111) SS BOND : bond 0.00473 ( 3) SS BOND : angle 0.98480 ( 6) covalent geometry : bond 0.00428 ( 3480) covalent geometry : angle 0.76402 ( 4731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8668 (mttm) cc_final: 0.8282 (mmtp) REVERT: A 171 PHE cc_start: 0.8098 (t80) cc_final: 0.7799 (t80) REVERT: A 185 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.7993 (p) REVERT: A 192 MET cc_start: 0.8331 (mmt) cc_final: 0.7609 (mmp) REVERT: A 193 LYS cc_start: 0.8493 (mppt) cc_final: 0.7872 (mppt) REVERT: A 194 GLN cc_start: 0.8152 (mp10) cc_final: 0.7929 (mp10) REVERT: A 216 LEU cc_start: 0.8918 (pt) cc_final: 0.8711 (pp) REVERT: A 246 GLU cc_start: 0.8458 (pt0) cc_final: 0.8250 (pt0) REVERT: B 136 ASP cc_start: 0.7595 (t0) cc_final: 0.7171 (t0) REVERT: B 138 GLN cc_start: 0.8516 (mt0) cc_final: 0.7996 (mm-40) REVERT: B 180 ARG cc_start: 0.3508 (mmp-170) cc_final: 0.2818 (mmp-170) REVERT: B 185 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8507 (p) REVERT: B 194 GLN cc_start: 0.8610 (mt0) cc_final: 0.7913 (mp10) REVERT: B 209 TYR cc_start: 0.4305 (OUTLIER) cc_final: 0.3069 (t80) REVERT: B 229 GLN cc_start: 0.8672 (mp-120) cc_final: 0.7797 (mp10) REVERT: B 246 GLU cc_start: 0.8570 (pt0) cc_final: 0.6966 (tp30) REVERT: C 124 LYS cc_start: 0.8427 (mtpp) cc_final: 0.7795 (mmtt) REVERT: C 187 ILE cc_start: 0.8058 (mm) cc_final: 0.7780 (pt) REVERT: C 194 GLN cc_start: 0.9032 (mt0) cc_final: 0.8645 (mp10) REVERT: C 207 MET cc_start: 0.7443 (tpt) cc_final: 0.7063 (ttp) REVERT: C 227 MET cc_start: 0.9030 (mpp) cc_final: 0.8606 (mtt) outliers start: 28 outliers final: 20 residues processed: 127 average time/residue: 0.1605 time to fit residues: 24.4400 Evaluate side-chains 126 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.138676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.125946 restraints weight = 5942.540| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 3.02 r_work: 0.4219 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 2.0536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3495 Z= 0.141 Angle : 0.864 12.396 4773 Z= 0.406 Chirality : 0.063 0.408 603 Planarity : 0.005 0.073 570 Dihedral : 8.156 51.057 699 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 6.35 % Allowed : 26.19 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 239 PHE 0.030 0.002 PHE B 171 TYR 0.016 0.001 TYR A 143 ARG 0.002 0.000 ARG A 140 Details of bonding type rmsd link_NAG-ASN : bond 0.01016 ( 12) link_NAG-ASN : angle 5.54517 ( 36) hydrogen bonds : bond 0.01595 ( 36) hydrogen bonds : angle 4.76990 ( 111) SS BOND : bond 0.00402 ( 3) SS BOND : angle 0.95318 ( 6) covalent geometry : bond 0.00311 ( 3480) covalent geometry : angle 0.71985 ( 4731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8596 (mttm) cc_final: 0.8273 (mmtp) REVERT: A 136 ASP cc_start: 0.7182 (t0) cc_final: 0.6793 (t0) REVERT: A 193 LYS cc_start: 0.8472 (mppt) cc_final: 0.7902 (mppt) REVERT: A 194 GLN cc_start: 0.8278 (mp10) cc_final: 0.8054 (mp10) REVERT: A 223 ASN cc_start: 0.8905 (t0) cc_final: 0.8653 (t0) REVERT: A 242 GLN cc_start: 0.9054 (pt0) cc_final: 0.8834 (pt0) REVERT: B 136 ASP cc_start: 0.7655 (t0) cc_final: 0.6982 (t0) REVERT: B 180 ARG cc_start: 0.3620 (mmp-170) cc_final: 0.2944 (mmp-170) REVERT: B 185 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8721 (p) REVERT: B 192 MET cc_start: 0.8194 (mpp) cc_final: 0.7910 (mpt) REVERT: B 194 GLN cc_start: 0.8726 (mt0) cc_final: 0.8412 (mp10) REVERT: B 209 TYR cc_start: 0.4514 (OUTLIER) cc_final: 0.2761 (t80) REVERT: B 246 GLU cc_start: 0.8513 (pt0) cc_final: 0.6856 (tp30) REVERT: C 122 ASP cc_start: 0.8619 (t0) cc_final: 0.8372 (t0) REVERT: C 124 LYS cc_start: 0.8387 (mtpp) cc_final: 0.7760 (mmtt) REVERT: C 170 GLN cc_start: 0.8920 (mt0) cc_final: 0.8472 (mt0) REVERT: C 187 ILE cc_start: 0.7786 (mm) cc_final: 0.7498 (pt) REVERT: C 194 GLN cc_start: 0.8982 (mt0) cc_final: 0.8162 (mp10) REVERT: C 207 MET cc_start: 0.7256 (tpt) cc_final: 0.6923 (ttp) REVERT: C 212 ASP cc_start: 0.7804 (m-30) cc_final: 0.7471 (m-30) REVERT: C 250 TYR cc_start: 0.9058 (t80) cc_final: 0.5788 (p90) outliers start: 24 outliers final: 17 residues processed: 125 average time/residue: 0.1609 time to fit residues: 23.9768 Evaluate side-chains 126 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 9.9990 chunk 26 optimal weight: 0.4980 chunk 33 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN C 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.137307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.124715 restraints weight = 5950.230| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 2.95 r_work: 0.4207 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 2.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3495 Z= 0.149 Angle : 0.870 12.174 4773 Z= 0.408 Chirality : 0.064 0.413 603 Planarity : 0.006 0.079 570 Dihedral : 7.948 50.661 699 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 5.82 % Allowed : 26.98 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 239 PHE 0.027 0.002 PHE B 171 TYR 0.015 0.001 TYR A 143 ARG 0.002 0.000 ARG A 140 Details of bonding type rmsd link_NAG-ASN : bond 0.01009 ( 12) link_NAG-ASN : angle 5.44390 ( 36) hydrogen bonds : bond 0.01687 ( 36) hydrogen bonds : angle 4.62794 ( 111) SS BOND : bond 0.00429 ( 3) SS BOND : angle 0.96294 ( 6) covalent geometry : bond 0.00334 ( 3480) covalent geometry : angle 0.73263 ( 4731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8636 (mttm) cc_final: 0.8305 (mmtp) REVERT: A 171 PHE cc_start: 0.8140 (t80) cc_final: 0.7772 (t80) REVERT: A 193 LYS cc_start: 0.8644 (mppt) cc_final: 0.8025 (mppt) REVERT: A 194 GLN cc_start: 0.8382 (mp10) cc_final: 0.8172 (mp10) REVERT: A 223 ASN cc_start: 0.8908 (t0) cc_final: 0.8649 (t0) REVERT: A 228 MET cc_start: 0.8995 (mtm) cc_final: 0.8513 (ttm) REVERT: B 138 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7899 (mm-40) REVERT: B 180 ARG cc_start: 0.3663 (mmp-170) cc_final: 0.2996 (mmp-170) REVERT: B 185 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8694 (p) REVERT: B 192 MET cc_start: 0.8455 (mpp) cc_final: 0.8133 (mpt) REVERT: B 194 GLN cc_start: 0.8774 (mt0) cc_final: 0.8468 (mp10) REVERT: B 209 TYR cc_start: 0.4667 (OUTLIER) cc_final: 0.3875 (t80) REVERT: B 246 GLU cc_start: 0.8643 (pt0) cc_final: 0.6884 (tp30) REVERT: C 122 ASP cc_start: 0.8744 (t0) cc_final: 0.8500 (t0) REVERT: C 124 LYS cc_start: 0.8403 (mtpp) cc_final: 0.7789 (mmtt) REVERT: C 170 GLN cc_start: 0.8917 (mt0) cc_final: 0.8606 (mt0) REVERT: C 187 ILE cc_start: 0.7913 (mm) cc_final: 0.7525 (pt) REVERT: C 194 GLN cc_start: 0.9026 (mt0) cc_final: 0.8210 (mp10) REVERT: C 207 MET cc_start: 0.7296 (tpt) cc_final: 0.6909 (mtp) REVERT: C 212 ASP cc_start: 0.7801 (m-30) cc_final: 0.7558 (m-30) outliers start: 22 outliers final: 17 residues processed: 121 average time/residue: 0.1538 time to fit residues: 22.2766 Evaluate side-chains 118 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.128070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.115899 restraints weight = 6130.567| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 2.90 r_work: 0.4105 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 2.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3495 Z= 0.205 Angle : 0.936 12.513 4773 Z= 0.441 Chirality : 0.066 0.446 603 Planarity : 0.006 0.086 570 Dihedral : 8.286 50.933 699 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 5.56 % Allowed : 28.57 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 239 PHE 0.028 0.002 PHE B 171 TYR 0.018 0.002 TYR B 135 ARG 0.003 0.000 ARG A 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00964 ( 12) link_NAG-ASN : angle 5.78208 ( 36) hydrogen bonds : bond 0.01814 ( 36) hydrogen bonds : angle 4.62934 ( 111) SS BOND : bond 0.00579 ( 3) SS BOND : angle 1.27506 ( 6) covalent geometry : bond 0.00466 ( 3480) covalent geometry : angle 0.79174 ( 4731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8634 (t0) cc_final: 0.8427 (t0) REVERT: A 124 LYS cc_start: 0.8705 (mttm) cc_final: 0.8382 (mmtp) REVERT: A 171 PHE cc_start: 0.8388 (t80) cc_final: 0.8149 (t80) REVERT: A 182 ASN cc_start: 0.8681 (m-40) cc_final: 0.8159 (t0) REVERT: A 194 GLN cc_start: 0.8497 (mp10) cc_final: 0.8196 (mp10) REVERT: A 228 MET cc_start: 0.9117 (mtm) cc_final: 0.8874 (ttm) REVERT: B 138 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8211 (mm-40) REVERT: B 180 ARG cc_start: 0.3683 (mmp-170) cc_final: 0.3015 (mmp-170) REVERT: B 194 GLN cc_start: 0.8869 (mt0) cc_final: 0.8565 (mp10) REVERT: B 209 TYR cc_start: 0.4895 (OUTLIER) cc_final: 0.4221 (t80) REVERT: B 246 GLU cc_start: 0.8681 (pt0) cc_final: 0.7056 (tp30) REVERT: C 122 ASP cc_start: 0.8805 (t0) cc_final: 0.8542 (t0) REVERT: C 124 LYS cc_start: 0.8384 (mtpp) cc_final: 0.7765 (mmtt) REVERT: C 168 GLN cc_start: 0.8209 (tt0) cc_final: 0.7756 (tt0) REVERT: C 170 GLN cc_start: 0.8764 (mt0) cc_final: 0.8235 (mt0) REVERT: C 187 ILE cc_start: 0.8308 (mm) cc_final: 0.7866 (pt) REVERT: C 193 LYS cc_start: 0.8900 (mttp) cc_final: 0.8377 (mtpp) REVERT: C 194 GLN cc_start: 0.9124 (mt0) cc_final: 0.8227 (mp10) REVERT: C 212 ASP cc_start: 0.7857 (m-30) cc_final: 0.7325 (m-30) outliers start: 21 outliers final: 16 residues processed: 112 average time/residue: 0.1617 time to fit residues: 21.6948 Evaluate side-chains 114 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN C 168 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.120038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.108044 restraints weight = 6537.514| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.94 r_work: 0.4018 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 2.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 3495 Z= 0.279 Angle : 1.032 12.861 4773 Z= 0.484 Chirality : 0.068 0.477 603 Planarity : 0.006 0.087 570 Dihedral : 9.120 50.258 699 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 5.56 % Allowed : 27.78 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 239 PHE 0.027 0.002 PHE B 171 TYR 0.018 0.002 TYR A 143 ARG 0.003 0.000 ARG A 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00987 ( 12) link_NAG-ASN : angle 6.54023 ( 36) hydrogen bonds : bond 0.01944 ( 36) hydrogen bonds : angle 4.82498 ( 111) SS BOND : bond 0.00833 ( 3) SS BOND : angle 1.70677 ( 6) covalent geometry : bond 0.00638 ( 3480) covalent geometry : angle 0.86328 ( 4731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8614 (t0) cc_final: 0.8414 (t0) REVERT: A 124 LYS cc_start: 0.8830 (mttm) cc_final: 0.8438 (mmtp) REVERT: A 171 PHE cc_start: 0.8570 (t80) cc_final: 0.8328 (t80) REVERT: A 182 ASN cc_start: 0.8792 (m-40) cc_final: 0.8335 (t0) REVERT: A 192 MET cc_start: 0.8576 (mmt) cc_final: 0.7904 (mmp) REVERT: A 194 GLN cc_start: 0.8614 (mp10) cc_final: 0.8190 (mp10) REVERT: B 138 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8113 (mm110) REVERT: B 180 ARG cc_start: 0.3824 (mmp-170) cc_final: 0.3578 (mmm160) REVERT: B 209 TYR cc_start: 0.5067 (OUTLIER) cc_final: 0.4553 (t80) REVERT: B 246 GLU cc_start: 0.8705 (pt0) cc_final: 0.7007 (tp30) REVERT: C 124 LYS cc_start: 0.8390 (mtpp) cc_final: 0.7771 (mmtt) REVERT: C 170 GLN cc_start: 0.8665 (mt0) cc_final: 0.8405 (mt0) REVERT: C 187 ILE cc_start: 0.8496 (mm) cc_final: 0.7968 (pt) REVERT: C 194 GLN cc_start: 0.9167 (mt0) cc_final: 0.8776 (mp10) REVERT: C 227 MET cc_start: 0.9173 (mmm) cc_final: 0.8817 (mtt) outliers start: 21 outliers final: 19 residues processed: 109 average time/residue: 0.1558 time to fit residues: 20.4871 Evaluate side-chains 112 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 242 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.130833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.118751 restraints weight = 6221.308| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 2.95 r_work: 0.4147 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 2.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3495 Z= 0.164 Angle : 0.954 12.389 4773 Z= 0.440 Chirality : 0.064 0.416 603 Planarity : 0.006 0.087 570 Dihedral : 8.900 50.216 699 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 5.03 % Allowed : 29.63 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 239 PHE 0.029 0.002 PHE B 171 TYR 0.017 0.001 TYR A 143 ARG 0.004 0.001 ARG C 140 Details of bonding type rmsd link_NAG-ASN : bond 0.01077 ( 12) link_NAG-ASN : angle 5.97665 ( 36) hydrogen bonds : bond 0.01681 ( 36) hydrogen bonds : angle 4.81375 ( 111) SS BOND : bond 0.00501 ( 3) SS BOND : angle 1.18293 ( 6) covalent geometry : bond 0.00364 ( 3480) covalent geometry : angle 0.80260 ( 4731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2001.04 seconds wall clock time: 35 minutes 11.50 seconds (2111.50 seconds total)